Preterm infants have altered body composition compared to term infants, which impacts both neurodevelopment and metabolic health, but whether increased dietary intake during hospitalization, independent of illness, may improve body composition is unknown. This prospective, longitudinal study (n = 103) measured fat-free mass (FFM) and percent body fat (%BF) at discharge and four months corrected age for prematurity (CA) in very low birth weight (VLBW) preterm infants. Markers of illness and macronutrient intakes (protein and caloric) were recorded. Bayley Scales of Infant Development-III (BSID) were administered at 12 and 24 months of age in a subset of these infants (n = 66 and n = 50 respectively). Body composition z-scores were calculated using recently developed reference curves. Linear regression was used to test the associations between clinical factors and body composition z-scores, as well as z-scores and BSID scores. Increased calories and protein received in the first week after birth and protein intake throughout hospitalization were associated with increased FFM z-scores at discharge, but not with %BF z-scores. After adjustment for both early acute and chronic illness, associations of nutrient intake with FFM z-score remained unchanged. FFM z-scores at discharge were positively associated with scores on the BSID at 12 and 24 months CA. In conclusion, increased energy and protein intakes both early in hospitalization and across its entire duration are associated with higher FFM at discharge, a key marker for organ growth and neurodevelopment in the VLBW neonate. Optimizing caloric intake, irrespective of illness is critical for enhancing body composition, and by extension, neurodevelopmental outcomes for preterm infants.